Tibetia himalaica
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA704171 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13594808_1.fastq.gz | Fastqsanger.gz | |||
| SRR13594808_2.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Transcriptome sequencing of Mirabilis himalaica
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Project description:Tibetia himalaica strain:Qinghai Raw sequence reads
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Project description:Crucihimalaya himalaica isolate:BT1 Genome sequencing and assembly
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Project description:Mirabilis himalaica (Nyctaginaceae) is endemic to the Himalayas where it is used in traditional Tibetan folk medicine. In this study, we first presented the complete chloroplast genome of M. himalaica. Complete genome size of M. himalaica ranged from 154,348 to 154,388?bp. The length varied from 85,808 to 85,845?bp in the (large single-copy) LSC region, from 17,935 to 17,938?bp in the (small single-copy) SSC region, and from 25,302 to 25,303?bp in the inverted repeat (IR) region. The overall GC contents of the chloroplast genome sequences were around 36%. Annotation analysis revealed a total of 112 genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis with three M. himalaica samples and five other Nyctaginaceae species showed that Mirabilis including two species was clustered with high bootstrap support. The complete chloroplast genome sequences obtained in this study will provide valuable data for wider studies into the phylogenetics and conservation biology of M. himalaica.
| S-EPMC7707768 | biostudies-literature
Project description:Crucihimalaya himalaica, a close relative of Arabidopsis and Capsella, grows on the Qinghai-Tibet Plateau (QTP) about 4,000 m above sea level and represents an attractive model system for studying speciation and ecological adaptation in extreme environments. We assembled a draft genome sequence of 234.72 Mb encoding 27,019 genes and investigated its origin and adaptive evolutionary mechanisms. Phylogenomic analyses based on 4,586 single-copy genes revealed that C. himalaica is most closely related to Capsella (estimated divergence 8.8 to 12.2 Mya), whereas both species form a sister clade to Arabidopsis thaliana and Arabidopsis lyrata, from which they diverged between 12.7 and 17.2 Mya. LTR retrotransposons in C. himalaica proliferated shortly after the dramatic uplift and climatic change of the Himalayas from the Late Pliocene to Pleistocene. Compared with closely related species, C. himalaica showed significant contraction and pseudogenization in gene families associated with disease resistance and also significant expansion in gene families associated with ubiquitin-mediated proteolysis and DNA repair. We identified hundreds of genes involved in DNA repair, ubiquitin-mediated proteolysis, and reproductive processes with signs of positive selection. Gene families showing dramatic changes in size and genes showing signs of positive selection are likely candidates for C. himalaica's adaptation to intense radiation, low temperature, and pathogen-depauperate environments in the QTP. Loss of function at the S-locus, the reason for the transition to self-fertilization of C. himalaica, might have enabled its QTP occupation. Overall, the genome sequence of C. himalaica provides insights into the mechanisms of plant adaptation to extreme environments.
| S-EPMC6452661 | biostudies-literature
Project description:Endophytic bacteria play important roles in medicinal plant growth, abiotic stress, and metabolism. Mirabilis himalaica (Edgew.) Heimerl is known for its medicinal value as Tibetan traditional plant; however, little is known about the endophytic bacteria associated with this plant in different geographic conditions and vegetal tissues. To compare the endophytic bacterial community associated with this plant in different geographic conditions and vegetal tissues, we collected the leaves, stems, and roots of M. himalaica from five locations, Nongmu college (NM), Gongbujiangda (GB), Zhanang County (ZL), Lang County (LX), and Sangri County (SR), and sequenced the 16S rRNA V5-V7 region with the Illumina sequencing method. A total of 522,450 high-quality sequences and 4970 operational taxonomic units (OTUs) were obtained. The different tissues from different locations harbored unique bacterial assemblages. Proteobacteria and Actinobacteria were the dominant phyla in all the samples, while the dominant genera changed based on the different tissues. The endophytic bacterial structures in the leaf and stem tissues were different compared to root tissues. Redundancy analysis (RDA) showed that the endophytic bacterial community was significantly correlated with pH, available phosphorus (AP), total phosphorus (TP), total nitrogen (TN), and soil organic matter (SOM). These findings suggested that the geographic conditions, climate type, ecosystem type, and tissues determined the endophytic bacterial composition and relative abundances. This conclusion could facilitate an understanding of the relationship and ecological function of the endophytic bacteria associated with M. himalaica and provide valuable information for artificial planting of M. himalaica and identifying and applying functional endophytic bacteria.
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